Recent progress in single-cell transcriptomic studies in plants

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Language: Английский

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Bioinformatics and AI/ML approaches using multi-omics data to accelerate diagnosis and delivery of precision care for patients with rare diseases

Methods in cell biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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Direct RNA sequencing in plants: practical applications and future perspectives

Plant Communications, Journal Year: 2024, Volume and Issue: 5(11), P. 101064 - 101064

Published: Aug. 18, 2024

The transcriptome serves as a bridge that links genomic variation to phenotypic diversity. A vast number of studies using next-generation RNA sequencing (RNA-seq) over the last 2 decades have emphasized essential roles plant in response developmental and environmental conditions, providing numerous insights into dynamic changes, evolutionary traces, elaborate regulation transcriptome. With substantial improvement accuracy throughput, direct (DRS) has emerged new powerful platform for precise detection native full-length transcripts, overcoming many limitations such read length PCR bias are inherent short-read RNA-seq. Here, we review recent advances dissecting complexity diversity transcriptomes DRS main technological approach, covering aspects metabolism, including novel isoforms, poly(A) tails, modification, propose comprehensive workflow processing data. Many challenges application plants, need machine learning tools tailored transcriptomes, remain be overcome, together outline future biological questions can addressed by DRS, allele-specific modification. This technology provides convenient support on which connection distinct features is tightly built, sustainably refining our understanding functions

Language: Английский

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Deciphering the Cell-Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 8, 2024

Abstract Cell fate determination during early embryonic development is a complex process modulated by gene expression. The intricate interplay of transcriptional and post-transcriptional regulation integral to the developmental trajectory embryogenesis, yet how RNA processing may contribute programming largely elusive. Leveraging recent technological advances in single-molecule nanopore sequencing, we developed single-cell long-read transcriptome sequencing technology, allowing clear view transcript diversity zebrafish embryogenesis pre- post-zygotic genome activation (ZGA). A closer examination dynamic usage potential alternative splicing revealed that abundant stage-specific transcripts with differential coding potentials are involved distinct biological functions. Specifically, identified two cell populations at onset ZGA based on isoform instead profiling, which followed divergent trajectories toward ectoderm presumptive ectoderm. These cells were characterized regulations linked RNA-binding proteins, including SNRPA SFPQ. Altogether, using strategy, work has cell-specific dynamics contributing embryogenesis.

Language: Английский

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Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 2, 2024

The advent of long-read (LR) sequencing technologies has provided a direct opportunity to determine the structure transcripts with potential for end-to-end full-length RNAs. LR methods that have been described date include commercial offerings from Oxford Nanopore Technologies (ONT) and Pacific Biosciences. These kits are based on selection polyadenylated (polyA+) RNAs and/or oligo-dT priming reverse transcription. Thus, these approaches do not allow comprehensive interrogation transcriptome due their exclusion non-polyadenylated (polyA-) In addition, polyA + specificity also results in 3'-biased measurements PolyA+ especially when RNA input is partially degraded. To address limitations current protocols, we modified rRNA depletion protocols used short-read sequencing: one approach representing ligation-based method other template-switch cDNA synthesis-based append ONT-specific adaptor sequences by removing any deliberate fragmentation/shearing RNA/cDNA. Here, present comparisons poly+ RNA-specific versions two including ONT PCR-cDNA Barcoding kit. displayed higher proportions (30%-50%) intronic content compared polyA-specific (5%-8%). enabled ∼20-50% detection expressed genes. Other metrics were favourable better coverage long transcripts, accuracy reproducibility expression measurements. Overall, indicate depletion-based here characterization While resulting reads enough help decipher transcript structures, future endeavors warranted improve proportion individual spanning transcripts.

Language: Английский

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scTrends: A living review of commercial single-cell and spatial 'omic technologies

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(12), P. 100723 - 100723

Published: Dec. 1, 2024

Understanding the rapidly evolving landscape of single-cell and spatial omic technologies is crucial for advancing biomedical research drug development. We provide a living review both mature emerging commercial platforms, highlighting key methodologies trends shaping field. This spans from foundational such as microfluidics plate-based methods to newer approaches like combinatorial indexing; on side, we consider next-generation sequencing imaging-based transcriptomics. Finally, highlight that may fundamentally expand scope data generation within pharmaceutical research, creating opportunities discover validate novel mechanisms. Overall, this serves critical resource navigating commercialization application in academic research.

Language: Английский

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